Author: OneAngstrom

Molecular modeling projects often grow in complexity over time: multiple molecules, intermediate results, test structures, images, scripts, and embedded data accumulate. It’s easy for things to become cluttered, which can slow down your workflow and make navigation difficult — especially…

If you’re a molecular scientist or educator working in an institutional environment, you’ve likely run into this frustration: installing scientific software often requires administrator rights. This can mean long delays while waiting for IT approval, unnecessary barriers when testing tools…

Creating molecular animations often comes with a simple but overlooked challenge: making a structure appear clearly and at the right time without visual noise. If you've ever tried to animate molecular models and show a molecule transitioning into the scene,…

When preparing a molecular animation for a presentation, publication, or educational material, a common challenge many researchers face is managing what the viewer sees—and what they don’t. Uncluttered visuals lead to greater clarity, but temporary removal and reappearance of molecular…

Molecular modelers often spend a great deal of time analyzing ligand unbinding pathways. Once paths are identified, it’s not uncommon to want to export the atomic coordinates corresponding to a subset of atoms moving along these paths—for example, to investigate…

Creating custom index groups is a recurring need in molecular simulations with GROMACS. Whether you are working on protein-ligand complexes, membrane systems, or free energy calculations, being able to define and reuse specific atom or residue groups simplifies analysis, facilitates…

When modeling complex molecular systems, selecting exactly the right atoms, residues, or chains can get tedious. Even with powerful selection tools, the process often involves clicking through multiple menus or remembering specific selection syntaxes. This becomes especially frustrating when you…

When you’re working on a molecular movie or educational demo, it’s often useful to make certain molecules or parts of a system disappear for a few moments. Maybe you want to reveal an internal binding site, or highlight a dynamic…

One of the common challenges molecular modelers face is adapting general-purpose parameter sets to the specific needs of their systems. Whether you’re simulating a novel peptide or working with non-standard residues, modifying molecular dynamics parameters (MDP parameters) is often essential.…